modules/samtools_ampliconclip

Clips read alignments where they match BED file defined regions

ampliconclippingampliconclipsamtools

https://github.com/nf-core/modules/[...]/modules/nf-core/samtools/ampliconclip

Description

Clips read alignments where they match BED file defined regions

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bed`
`:file`

BED file of regions to be removed (e.g. amplicon primers)

*.{bed}

`save_cliprejects`
`:boolean`

Save filtered reads to a file

`save_clipstats`
`:boolean`

Save clipping stats to a file

Output

name:type

description

pattern

`bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.clipallowed.bam`
`:file`

Clipped reads BAM file

*.{bam}

`stats`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.clipstats.txt`
`:file`

Clipping statistics text file

*.{clipstats.txt}

`rejects_bam`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.cliprejects.bam`
`:file`

Filtered reads BAM file

*.{cliprejects.bam}

`versions_samtools`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools version | sed '1!d;s/.* //'`
`:eval`

The expression to obtain the version of the tool

Tools

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

modules/samtools_ampliconclip

Description

Input

`meta`
`:map`

`bam`
`:file`

`bed`
`:file`

`save_cliprejects`
`:boolean`

`save_clipstats`
`:boolean`

Output

`bam`

`meta`
`:map`

`*.clipallowed.bam`
`:file`

`stats`

`meta`
`:map`

`*.clipstats.txt`
`:file`

`rejects_bam`

`meta`
`:map`

`*.cliprejects.bam`
`:file`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

Tools

samtools
MIT

maintainers

get in touch

modules/samtools_ampliconclip

Description

Input

meta:map

bam:file

bed:file

save_cliprejects:boolean

save_clipstats:boolean

Output

bam

meta:map

*.clipallowed.bam:file

stats

meta:map

*.clipstats.txt:file

rejects_bam

meta:map

*.cliprejects.bam:file

versions_samtools

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Topics

versions

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':eval

Tools

samtools MIT

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bed`
`:file`

`save_cliprejects`
`:boolean`

`save_clipstats`
`:boolean`

`bam`

`meta`
`:map`

`*.clipallowed.bam`
`:file`

`stats`

`meta`
`:map`

`*.clipstats.txt`
`:file`

`rejects_bam`

`meta`
`:map`

`*.cliprejects.bam`
`:file`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

`versions`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:eval`

samtools
MIT